This R03 proposal will develop and standardize an appropriate clinical and laboratory approach to investigating potential infectious etiologies of pediatric Crohn's disease (CD). We aim to standardize specimen procurement, processing and testing with unique, validated laboratory assays to detect select infectious agents in pediatric intestinal biopsies, and evaluate the appropriateness of different control specimens. Future studies to test whether infection(s) cause pediatric CD or determine its morbidity demand these tools and methods. CD pathobiology is unclear. It has been proposed that one or more infectious agents precipitate CD in a genetically susceptible host and it may be easier to identify some agents in childhood CD. Current scientific evidence does not prove causality, despite research on a number of specific microbes (e.g., enteroadherent Escherichiae coli, measles virus). To test infectious hypotheses, valid diagnostic tools must be developed and tested in well-characterized cohorts of children as well as adults employing uniform case and control definitions. Differences between childhood and adult onset CD might signify risk factor differences: children can have more severe intestinal disease, increased risk of colon cancer and earlier complication onset. Children, particularly with new onset disease, may represent a unique population to study environmental factors (e.g., infection), since younger age brings shorter and less complicated exposure histories to confound analyses. The Pediatric IBD Consortium of 6 large, geographically diverse U.S. centers represents an excellent platform to investigate potential infectious triggers of CD, evaluating and recording clinical and epidemiologic data on approximately 288 newly diagnosed pediatric CD cases per year in a comprehensive database. Our application proposes that adequate collection of intestinal biopsies from uniformly-defined Consortium cases and controls and validation of sensitive and specific laboratory tools to detect potential infectious triggers of CD in such specimens can be achieved. Our R03 aims to: 1) standardize collection (e.g., anatomic source), processing and banking of gastrointestinal biopsies obtained during clinically-indicated endoscopy of well-characterized children with CD and well-characterized controls; 2) define, standardize and verify "appropriate" controls, "non-diseased" biopsies from cases vs. clinically-indicated biopsies from children without IBD (e.g., Hirschsprung's disease); 3) standardize and validate detection of certain infectious agents in these specimens through pathology-based (IHC, ISH), broad-range amplification-based (PCR) and organism-specific (e.g., MAP) molecular analysis complemeted by culture for MAP and localization of pathogens within diseased tissue. Parallel comparisons of intestinal biopsies to gene arrays on stool specimes from cases and controls to ascertain the role of indigenous colonic microflora will also be performed. Subsequent prospective application of methods and systems developed by this proposal to the uniquely large, well characterized Consortium cohort will optimize detecting differences between CD and non-disease.